Announcing Progenesis SDF Studio

We’re excited to announce the release of the Progenesis SDF Studio – a free tool for the viewing and editing of SDF and MOL files.

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Why was it developed?

One of the major bottlenecks in LC-MS metabolomics data analysis is identification – something that our latest release of Progenesis QI has targeted by adding more search methods – and one of the biggest issues is sourcing a suitable database for your study. The number of publicly available databases is increasing, but unfortunately not all of these files are correctly formatted. Without some intervention, they can’t be used for identification.

Of course, the MetaScope search engine in Progenesis also allows the searching of Excel databases, which are much easier to fix. However, these are of no use if you want to perform theoretical fragmentation (which requires structure information), or if you want to use an alternative piece of software. After supporting a number of our users by fixing errors in their SDFs, we realised that there’s a distinct lack of a free and easy-to-use SDF editor. While we were happy to carry on fixing these files on behalf of our users, we realised the benefits that such an editor could bring to the wider community. So, here it is: v0.9 of Progenesis SDF Studio.

Why version 0.9?

This first release of Progenesis SDF Studio is an early access edition – we want your feedback on it so we can make tailored improvements before we release v1.0. That’s not to say we’ll stop there; we’ll keep on making changes and issuing new releases based on your feedback, but we wanted to make it clear that we’d value your input on how we should develop the tool in the future. So tell us:

  • Is it easy to use? Which bits could be made easier?
  • Is it missing some functionality you’d like?
  • Does it have functionality that’s not required?
  • Anything else!

What does it do?

The Progenesis SDF Studio allows you to:

  • View your SDFs and MOL files – search to find out whether your database contains the compounds you’re interested in
  • Delete entries – allows you to reduce a database down to only the compounds in which you’re interested
  • Combine SDFs and MOL files – in case you can’t find a single database containing all of your compounds of interest
  • Correct any formatting errors (including automatic highlighting of entries with errors) – fix any formatting problems that are causing your compound ID search to fail

How can I get it?

You can download Progenesis SDF Studio here. And did I mention it’s free? Yes, FREE.

How will I know how to use it?

We’ve written a small number of anticipated FAQ articles which outline some basic concepts – we’ll add to these as your questions come in. Our support team will also be on hand to help with any queries about this early access edition.